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Home » Recipes » Healthy Muffin Recipes

Healthy peanut butter and jelly muffins

By: Kathryn Doherty | Last Updated: Mar 6, 2025 | Published: Mar 2, 2017
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Healthy peanut butter and jelly muffins are whole wheat and naturally sweetened, with no butter or oil but plenty of peanut butter flavor and a fun jelly center!Peanut butter muffins with jelly inside on a brown parchment paper with a spoon full of jelly resting nearby.

I think by now you guys know we are ALL about some muffins in this house.

I probably bake at least 2 batches of muffins a week, more on weeks when we’ve run out and I’m replenishing our freezer stock.

(Just watch my Instagram stories on the weekends…)

Muffins. All. Day. Long. (Including for dinner, like my veggie mac and cheese muffins I re-shared earlier in the week.)

Peanut butter muffin batter in a muffin tin with dollops of jelly in the middle A muffin tin filled with peanut butter muffin batter

These healthy peanut butter and jelly muffins are our current obsession. They are whole wheat and naturally sweetened (like many of my muffins - see my muffin category) and a great addition to school lunches.

And if your school is peanut-free, you can absolutely sub almond butter here. I’ve done them that way too. (M’s kindergarten class is OK with peanut products but J’s preschool is completely peanut-free.)

You can check out the video above to see how I make these and keep the jelly in the middle of the muffin.

Basically you fill the muffin tins with a bottom layer of the peanut butter dough, then dollop a teaspoon of jelly in the middle of each cup and cover it up with another layer of peanut butter dough. This keeps the jelly in the center of each muffin.

Wanna know what happens if you don’t do this carefully and cover up all the jelly?

Peanut butter and jelly muffins on a plate with one muffin cut in half

 Nothing. Nothing happens. Some of the jelly leaks out the sides of the muffins and gets oozy everywhere. It actually looks pretty cool. It’s no longer a hidden gem in the middle of the muffin, but sometimes, you gotta glob it in there and go, no time to fuss with arranging dough and jelly.

I get it.

Notes on healthy peanut butter and jelly muffins:

  • As I mentioned, you can substitute almond butter for these muffins if you have a child with a food allergy or you're sending the muffins to a nut-free school.
  • These are great for breakfast, for school lunches, for an afternoon snack or just for having on hand when you need an energy boost.
  • If you really want a lot of peanut butter flavor, add a smear on top when you serve these.
  • Also, I used my easy strawberry freezer jam cause I always have some in the fridge or freezer, but you can use a store-bought jelly and make these with any of your favorite flavors.

Side note: I grew up on grape jelly. Or so I thought. Once I was an adult and came home to stay I looked at the actual label and discovered it was blackberry.

I’d been eating blackberry jelly all my life thinking it was grape. #gamechanger #icanttrustanythinganymore #whatelsedontIknowabout)

OK, drama moment over...

Half of a peanut butter muffin with a jelly filling being held

The other great thing about these, as with most muffins, is they store beautifully!

How to store PB&J muffins:

- These peanut butter and jelly muffins will keep covered, on the counter, for up to 3 days or in the refrigerator for up to 5 days.

- You can also freeze the extras. Let the muffins cool completely. Place them in a freezer-safe ziptop bag (that’s labeled!) and freeze for up to 6 months.

- I like to wrap muffins individually in aluminum foil before putting them into the bag. It adds an extra layer of protection from freezer burn.

- To thaw, just place one or more muffins in the refrigerator overnight. Serve cold from the fridge or warm in the microwave for about 15-20 seconds.

- You can also warm a muffin in the microwave straight from the freezer in a pinch. Start with 45 seconds and add time (and possibly turn it upside down) as needed.

So join me in the kitchen and make some muffins. And then some more. And then 32,000 more batches.

Enjoy!

XO,

Kathryn

A halved peanut butter and jelly muffin on a white plate with extra jelly on the side.
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4.67 from 9 votes

Healthy peanut butter and jelly muffins

Healthy peanut butter and jelly muffins are whole wheat and naturally sweetened, with no butter or oil but plenty of peanut butter flavor and a fun jelly center!
Prep Time14 minutes mins
Cook Time16 minutes mins
Total Time30 minutes mins
Yield: 12 muffins

Ingredients

  • 1 ½ cups white whole wheat flour
  • 1 teaspoon baking soda
  • ¼ teaspoon baking powder
  • ½ teaspoon cinnamon
  • ½ teaspoon salt
  • 2 large eggs
  • ⅔ cup creamy peanut butter
  • ½ cup honey
  • ½ cup unsweetened applesauce
  • ¼ cup milk
  • 1 teaspoon vanilla
  • ¼ cup fruit jam, divided

Instructions

  • Preheat oven to 350. Line a muffin tin with paper liners, then spray with cooking spray and set aside.
  • In a large bowl, combine flour, baking soda, baking powder, cinnamon and salt.
  • In a separate bowl, add eggs, peanut butter, honey, applesauce, milk and vanilla and stir until well combined.
  • Add the wet mixture to the bowl with the dry ingredients and stir until just combined. The batter will be thick.
  • Fill each lined muffin cup about ⅓ full with the peanut butter dough. Wet your fingers and use them to press the mixture down and cover the bottom of each muffin tin.
  • Spoon about 1 teaspoon of jam or jelly into the middle of each cup.
  • Cover each cup with another dollop of peanut butter dough until all the dough is used. 
  • Use wet fingers to pat down the tops of the muffins and seal in the jelly filling.
  • Bake at 350 for 16-18 minutes, until a toothpick inserted in the center comes out clean.
  • Cool the muffins on a wire rack then store at room temperature for 2-3 days, in the refrigerator for up to 5 days or in the freezer for up to 5 months.

Notes

You can use white wheat flour or use whole wheat flour. You can also use a mix of whole wheat flour and all-purpose flour if you prefer.
You can substitute almond butter for the peanut butter to make these peanut-free if needed.
You can use 2% milk, skim milk, soy milk - whatever you have.
I use my easy strawberry freezer jam, but you can use a store-bought jelly and make these with your favorite flavor of jelly.

Video

Nutrition

Serving: 1muffin | Calories: 217kcal | Carbohydrates: 32g | Protein: 6g | Fat: 8g | Saturated Fat: 2g | Polyunsaturated Fat: 5g | Cholesterol: 31mg | Sodium: 289mg | Fiber: 3g | Sugar: 17g
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!
A collage of peanut butter and jelly muffins in baking pans and then set on brown parchment paper with a text box in the middle.

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Reader Interactions

Comments

  1. Cheyanne @ No Spoon Necessary

    March 02, 2017 at 10:19 am

    5 stars
    Well I need to come over to your house, because muffins all day, every day is my idea of a great time! 🙂 I am loving these PB & J muffins, girlfriend! That jelly center is so fun!!! Seriously, this is taking PB & J to a whole new, delicious level! I could definitely eat these on repeat... which is totally acceptable since they are healthified! Yay! Pinned! Cheers chicka!

    Reply
    • Kathryn

      March 02, 2017 at 8:40 pm

      Come on over, girl! We are always stocked up on muffins! XO

      Reply
  2. Adina

    March 04, 2017 at 1:19 pm

    5 stars
    Delicious looking muffins, I love the jam inside. I've never heard of a peanut-free school or kindergarten, it makes sense considering how dangerous peanuts can be for allergic people. I am happy that our kindergarten is sugar-free.

    Reply
    • Kathryn

      March 05, 2017 at 8:27 am

      Thanks Adina! A lot of schools here in the U.S. are peanut-free or have peanut-free classrooms to keep kids with allergies safe. But I love the idea of a sugar-free kindergarten!

      Reply
  3. Kate @ Framed Cooks

    March 05, 2017 at 9:42 am

    Okay, these look AMAZING. The jelly in the middle? Just plain heaven.

    Reply
    • Kathryn

      March 05, 2017 at 9:19 pm

      Thanks so much Kate! 😊

      Reply
  4. Veronika

    May 22, 2017 at 10:53 am

    What a great idea to put jam inside! These muffins look scrumptious! Will definitely try this recipe.

    Reply
    • Kathryn

      May 23, 2017 at 8:36 pm

      It's a fun little surprise! I hope you love them Veronika! 😊

      Reply
  5. Claire

    January 11, 2018 at 5:00 pm

    Please tell me that you used natural peanut butter! I know that sometimes it is not recommended for baking because of texture but it's the only PB we eat as there's nothing added. I'd hate to have to buy the sugar laden one!

    Reply
    • Kathryn

      January 11, 2018 at 5:38 pm

      Hi Claire! Yes, I use a natural peanut butter with no added sugar. Just peanuts and a pinch of salt. I hope that helps and I hope you enjoy these muffins!

      Reply
  6. Lindsay Cotter

    February 27, 2019 at 10:54 pm

    What a fun make ahead breakfast! These are perfect for a quick morning breakfast!

    Reply
    • Kathryn

      March 01, 2019 at 9:35 am

      They are so fun! We love them for breakfast, lunch and snacking too! A great on-the-go muffin!

      Reply
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Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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